Zinc in PDB 7t9x: Saccharomyces Cerevisiae PEX12 Ring Domain

The structure of Saccharomyces Cerevisiae PEX12 Ring Domain, PDB code: 7t9x was solved by P.Feng, T.Rapoport, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	71.22 / 1.52
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	27.578, 32.922, 72.488, 90, 100.72, 90
R / Rfree (%)	18.6 / 19.7

The binding sites of Zinc atom in the Saccharomyces Cerevisiae PEX12 Ring Domain (pdb code 7t9x). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Saccharomyces Cerevisiae PEX12 Ring Domain, PDB code: 7t9x:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Saccharomyces Cerevisiae PEX12 Ring Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Saccharomyces Cerevisiae PEX12 Ring Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn101 b:13.4 occ:0.75 SG A:CYS13 2.3 13.3 1.0 SG A:CYS33 2.4 12.2 1.0 SG A:CYS10 2.4 10.8 1.0 SG A:CYS30 2.4 12.9 1.0 CB A:CYS10 3.1 14.1 1.0 CB A:CYS30 3.2 10.9 1.0 CB A:CYS33 3.2 11.9 1.0 CB A:CYS13 3.3 15.0 1.0 N A:CYS13 3.8 13.8 1.0 N A:CYS30 3.9 11.5 1.0 CA A:CYS13 4.1 13.5 1.0 CA A:CYS30 4.2 12.1 1.0 O A:HOH236 4.3 22.3 1.0 CA A:CYS10 4.5 13.8 1.0 CB A:VAL12 4.7 12.1 1.0 CA A:CYS33 4.7 12.3 1.0 C A:VAL12 4.9 15.6 1.0 C A:CYS13 4.9 15.0 1.0

Zinc binding site 2 out of 2 in the Saccharomyces Cerevisiae PEX12 Ring Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Saccharomyces Cerevisiae PEX12 Ring Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn101 b:13.8 occ:0.80 SG B:CYS33 2.3 11.7 1.0 SG B:CYS13 2.3 13.3 1.0 SG B:CYS30 2.3 12.6 1.0 SG B:CYS10 2.4 10.4 1.0 CB B:CYS10 3.1 12.8 1.0 CB B:CYS30 3.2 10.1 1.0 CB B:CYS33 3.3 10.2 1.0 CB B:CYS13 3.3 15.7 1.0 N B:CYS13 3.8 14.0 1.0 N B:CYS30 3.9 10.2 1.0 CA B:CYS13 4.1 14.2 1.0 CA B:CYS30 4.2 10.0 1.0 O B:HOH234 4.3 25.2 1.0 O B:HOH232 4.3 25.4 1.0 CA B:CYS10 4.6 13.3 1.0 CB B:VAL12 4.7 13.1 1.0 CA B:CYS33 4.7 10.5 1.0 C B:VAL12 4.9 16.1 1.0 C B:CYS13 4.9 17.1 1.0

P.Feng, X.Wu, S.K.Erramilli, J.A.Paulo, P.Knejski, S.P.Gygi, A.A.Kossiakoff, T.A.Rapoport. A Peroxisomal Ubiquitin Ligase Complex Forms A Retrotranslocation Channel. Nature V. 607 374 2022.
ISSN: ESSN 1476-4687
PubMed: 35768507
DOI: 10.1038/S41586-022-04903-X